PeerJ最新文献

{"title":"Longitudinal effects of aerobic training programme on body composition in non-elite adolescent female swimmers.","authors":"Mariusz Kuberski, Agnieszka Musial, Maciej Choroszucho, Jan M Konarski, Jacek Wąsik","doi":"10.7717/peerj.19456","DOIUrl":"10.7717/peerj.19456","url":null,"abstract":"<p><strong>Introduction: </strong>The aim of this study was to assess the impact of a 3-year swimming training programme on body fat measurements in adolescent girls, without prior selection.</p><p><strong>Method: </strong>Two groups of 10-year-old girls were analysed at the beginning of the study (4th grade in primary school). The experimental group consisted of 14 swimmers (body mass: 34.99 ± 2.77 kg; height: 146.00 ± 3.05 cm). The control group consisted of 14 girls (body mass: 37.93 ± 6.02 kg; height: 145.55 ± 3.88 cm) who only participated in mandatory physical education classes. The study was conducted over a period of 3 years, with measurements taken every 6 months. Body fat was measured through the thickness of skinfolds at four anatomical locations: above the biceps; above the triceps; below the lower angle of the scapula; and above the superior iliac crest. Based on these measurements, the percentage of body fat was calculated.</p><p><strong>Results: </strong>Statistical analysis revealed that despite the lack of initial selection, there was no significant difference in the percentage of body fat between the experimental and control groups at the start of the study-18.62% <i>vs</i> 24.85%. This difference persisted until the final measurement after 3 years, at which point it became statistically significant-17.31% <i>vs</i> 27.14% (F = 37.44, <i>p</i> < 0.05).</p><p><strong>Discussion: </strong>Our findings indicate that 3 years of swimming training in adolescent girls resulted in a reduction in fat tissue growth across all four measurement sites. Initially, body fat percentage had a strong negative impact on VO₂ max, particularly in the experimental group. However, this effect diminished in both groups over the course of the study.</p><p><strong>Conclusion: </strong>Swimming may be an effective means of preventing obesity. Coaches should consider a slim physique in swimming candidates.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e19456"},"PeriodicalIF":2.3,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12097237/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144128218","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Association between non-alcoholic fatty liver disease and arterial stiffness measured by brachial-ankle pulse wave velocity: a cross-sectional population study.","authors":"Yujie Wang, Zhicheng Fang, Qiuyue Fu, Dongai Yao, Xiaoqing Jin","doi":"10.7717/peerj.19405","DOIUrl":"10.7717/peerj.19405","url":null,"abstract":"<p><strong>Background: </strong>Non-alcoholic fatty liver disease (NAFLD) is strongly linked with metabolic syndrome and atherosclerotic cardiovascular diseases (ASCVDs). This study aimed to assess the feasibility of using brachial-ankle pulse wave velocity (baPWV), a non-invasive technique, to monitor atherosclerosis (AS) in NAFLD patients and to evaluate the AS risk in various sub-populations of NAFLD patients.</p><p><strong>Materials and methods: </strong>A cross-sectional study was conducted with 4,844 participants, enrolled from January 1, 2019, to December 31, 2021, at the Physical Examination Center of Zhongnan Hospital of Wuhan University. Participants were aged 18 to 88 years. According to the main points of the ultrasonic diagnosis of NAFLD, the ultrasonic image report was made for the subjects. AS is defined as baPWV ≥ 1,400 cm/s. We used multiple logistic regression analysis to explore the relationship between NAFLD and AS, and multiple linear regression analysis to explore the correlation between NAFLD and baPWV by modeling. Subgroup analysis was performed based on age and gender to adjust for confounding bias and complete sensitivity analysis.</p><p><strong>Results: </strong>The prevalence of NAFLD was 38.3% in all participants, with 45.4% in men and 25.1% in women. Among the overall NAFLD population and male NAFLD patients, baPWV exceeded the diagnostic threshold for AS (1,419.70 ± 205.51, 1,429.71 ± 196.13) starting from the 45-55 age group. Through the analysis of the age-baPWV scatter plots and fitted lines, along with sensitivity analysis, it is recommended that male patients should start monitoring at 46 years old for AS using baPWV, while female patients should begin at 51 years old. NAFLD was associated with increased odds of AS (OR: 1.206, 95% CI [1.021-1.423], <i>P</i> = 0.027) after adjusting for confounders. NAFLD was independently positively correlated with baPWV (Model 2: <i>β</i> = 0.086, Δ<i>R</i> ² = 0.006, <i>P</i> < 0.001; Model 3: <i>β</i> = 0.05, <i>P</i> < 0.001). This positive correlation was also observed in both males and females (male: Model 2: <i>β</i> = 0.081, Δ<i>R</i> ² = 0.005, <i>P</i> < 0.001; Model 3: <i>β</i> = 0.052, <i>P</i> = 0.001; female: Model 2: <i>β</i> = 0.088, Δ<i>R</i> ² = 0.006, <i>P</i> < 0.001; Model 3: <i>β</i> = 0.042, <i>P</i> = 0.02).</p><p><strong>Conclusion: </strong>NAFLD demonstrated an independent association with AS assessed via baPWV, an accessible non-invasive tool for early AS evaluation. Regular baPWV monitoring is recommended for NAFLD patients > 45 years, with males and females initiating surveillance at 46 and 51 years, respectively. Study limitations, including potential biases in NAFLD diagnosis, gender distribution imbalances, and confounding variable interdependencies, necessitate further stratified population analyses.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e19405"},"PeriodicalIF":2.3,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12097236/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144128059","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Stochastic processes dominate the community assembly of ectomycorrhizal fungi associated with <i>Betula platyphylla</i> in Inner Mongolia, China.","authors":"Min Li, Zhaoyun Meng, Jinyan Li, Xuan Zhang, Yonglong Wang, Xinyu Li, Yuze Yang, Yue Li, Xunjue Yang, Xiuli Chen, Yongjun Fan","doi":"10.7717/peerj.19364","DOIUrl":"10.7717/peerj.19364","url":null,"abstract":"<p><p>The maintenance and driving mechanisms of microbial community structure have become important research focuses in microbial ecology. Therefore, clarifying the assembly of ectomycorrhizal (EM) fungal communities can provide a relevant basis for studying forest diversity, ecological diversity, and ecological evolution. <i>Betula platyphylla</i> is a typical EM dependent tree species with characteristics such as renewal ability and strong competitive adaptability, and it plays a crucial ecological function in Inner Mongolia. However, the research on EM fungi's diversity and community assembly is very limited. We investigated EM fungal communities associated with <i>B. platyphylla</i> from 15 rhizosphere soil samples across five sites in Inner Mongolia. The fungal rDNA ITS2 region was sequenced using Illumina Miseq sequencing. A total of 295 EM fungal OTUs belonging to two phyla, three classes, nine orders, 20 families, and 31 genera were identified, of which <i>Russula</i>, <i>Cortinarius</i>, and <i>Sebacina</i> were the most dominant taxa. Significant differences existed in the composition of dominant genera of EM fungi across the five sites, and the relative abundances of dominant genera also showed significant differences among the sites. The β NTI and NCM fitting analyses suggest that stochastic processes mainly determine the EM fungal community assembly. Our study indicates that <i>B. platyphylla</i> harbors a high EM fungal diversity and highlights the important role of the stochastic process in driving community assembly of mutualistic fungi associated with <i>B. platyphylla</i> in north China.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e19364"},"PeriodicalIF":2.3,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12097238/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144128204","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effect of whole-body vibration training on bone mineral density in older adults: a systematic review and meta-analysis.","authors":"Danilo A Massini, Tiago A F Almeida, Anderson G Macedo, André B Peres, Víctor Hernández-Beltrán, José M Gamonales, Mário C Espada, Cassiano M Neiva, Dalton M Pessôa Filho","doi":"10.7717/peerj.19230","DOIUrl":"10.7717/peerj.19230","url":null,"abstract":"<p><strong>Background: </strong>Whole-body vibration (WBV) aims to increase bone mineral density (BMD) using vertical mechanical accelerations from the plantar surface of the feet through the muscles and bones. A vibration platform is used for this purpose. This systematic review (PROSPERO-CRD 42023395390) analysed the effects of WBV training on BMD at anatomical sites most affected by osteoporotic fractures in older adults.</p><p><strong>Methodology: </strong>Systematic searches were conducted in the databases. Randomized controlled studies quantifying aerial BMD (aBMD) using the dual-energy X-ray absorptiometry method before and after WBV training in adults aged 55 and older were included. Independent reviewers performed methodological quality analysis (TESTEX) and assessed the risk of bias, and the GRADE scale determined the certainty of evidence in the results of the selected studies. The aBMD values from anatomical sites in the femoral neck, total proximal femur, and lumbar spine from WBV training protocols were included in the meta-analysis. The forest plot was generated using the random-effects model, and the effect size was measured by Hedges' <i>g</i>.</p><p><strong>Results: </strong>Seven studies involving 202 participants were included, with TESTEX = 12.6 (excellent quality) and risk of bias (43% low risk, and 57% some concerns), demonstrating with low heterogeneity, a significant effect of WBV training on total femur aBMD (<i>g</i> = 0.28 (small), <i>p</i> = 0.04). However, in spite of the low heterogeneity, the femoral neck (<i>g</i> = 0.15 (trivial), <i>p</i> = 0.19) and lumbar spine (<i>g</i> = 0.13 (trivial), <i>p</i> = 0.31) regions did not show a significant effect with WBV training.</p><p><strong>Conclusions: </strong>The results showed with low certainly evidence that WBV training had a statistically significant effect on total femur aBMD but not on femoral neck and lumbar spine.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e19230"},"PeriodicalIF":2.3,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12087579/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144102387","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Adult picky eating and associations with childhood picky eating, maternal feeding, aversive sensory responsiveness, disgust and obsessive-compulsive symptoms.","authors":"Ada H Zohar, Dorin Barhum Shapira, Lilac Lev-Ari, Rachel Bachner-Melman","doi":"10.7717/peerj.19444","DOIUrl":"10.7717/peerj.19444","url":null,"abstract":"<p><strong>Background: </strong>Adult picky eating (PE) can cause distress, malfunction, and malnutrition. The purpose of this study was to examine adult PE, its relationship to childhood PE and to symptoms of obsessive-compulsive disorder (OCD), sensory processing disorder, food and general disgust, and maternal child feeding practices.</p><p><strong>Methods: </strong>Adult participants (<i>N</i> = 772; 636 women) self-reported on measures of adult PE (Adult Picky Eating Questionnaire (APEQ)), obsessive-compulsive symptoms (Obsessive-Compulsive Inventory-Revised (OCI-R)), sensory processing difficulties (Sensory Responsiveness Questionnaire-Intensity Scale (SRQ-IS)), general disgust propensity (Disgust Propensity and Sensitivity Scale-12 (DPSS-12)), food disgust (Food Disgust Scale-short (FDS-S)), and three maternal feeding practices (Retrospective Child Feeding Questionnaire (RCFQ)).</p><p><strong>Results: </strong>Childhood PE and current adult PE were strongly associated. Adults with PE who scored in the top 25 percentile on the APEQ were at risk for OCD and sensory processing disorder; most reported having been picky eaters in childhood. Structural equation modelling with good fit indices confirmed a developmental model in which general disgust, food disgust and sensory processing difficulties contributed to childhood PE and maternal feeding practices (pressure to eat, restriction), which in turn contributed to OCD symptoms. In addition, pressure to eat, restriction and OCD symptoms contributed directly to adult PE.</p><p><strong>Conclusions: </strong>Severe adult PE is related to childhood PE and disgust sensitiviy, OCD and sensory processing disorder. Adults with severe PE may meet criteria for adult avoidant restrictive feeding or eating disorders. For adults with extreme PE clinical intervention may be warranted.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e19444"},"PeriodicalIF":2.3,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12087578/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144102350","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic variability and trait associations for physiological and agronomic characteristics in bread wheat genotypes under drought stress and well-watered conditions.","authors":"Mohammed O Alshaharni, Fatmah A Safhi, Nora M Al Aboud, Dmitry E Kucher, Eman Fayad, Mohammed Alqurashi, Rahmah N Al-Qthanin, Ibtesam S M Almami, Heba I Ghamry, Diaa Abd El-Moneim, Mohamed M Kamara, Abdelraouf M Ali","doi":"10.7717/peerj.19341","DOIUrl":"10.7717/peerj.19341","url":null,"abstract":"<p><p>Drought is a critical abiotic stress significantly reducing global wheat production, especially under climate fluctuations. Investigating wheat genetic variability using physiological and agronomic characteristics is essential for advancing breeding to enhance drought resilience and ensure sustainable production in light of global population growth. The genetic diversity and associations among traits of fourteen diverse genotypes of bread wheat in drought-stressed and well-watered conditions were studied, focusing on physiological and agronomic responses. Significant variations were detected among irrigation regimes, genotypes, and their interactions for all assessed characteristics. Drought stress substantially declined chlorophyll <i>a</i> (Chl <i>a</i>) and <i>b</i> (Chl <i>b</i>), net photosynthetic rate (NPR), transpiration rate (Tr), stomatal conductance (gs), membrane stability index (MSI), relative water content (RWC), plant height (PH), yield-related attributes, and grain yield. Conversely, it significantly increased malondialdehyde content, proline content (ProC), and activities of antioxidant enzymes, including catalase (CAT), ascorbate peroxidase (APX) and superoxide dismutase (SOD). The genotypes, G3 (L-1117), G8 (L-120), and G12 (L-1142) exhibited superior drought tolerance, maintaining high photosynthetic efficiency, RWC, antioxidant enzyme activity, and grain yield. Under drought conditions, these genotypes achieved grain yields of 6.32 t/ha (G8), 5.97 t/ha (G12), and 5.84 t/ha (G3), significantly surpassing the other genotypes. Genotypic classification and drought tolerance indices confirmed the superiority of G3, G8, and G12 as drought-resilient candidates, while G2, G5, G7, and G14 exhibited lower adaptability. Genotypic stability analysis (additive main effects and multiplicative interaction (AMMI) and ranking biplot) indicated that G3, G8, G6, and G12 were highly stable across diverse environments, making them promising candidates for wheat breeding programs. Agronomic traits such as PH, number of grains per spike (NGPS), and thousand kernel weight (TKW) were positively associated with drought tolerance. Furthermore, the multivariate analyses, including principal component analysis (PCA), correlation, and path analysis, highlighted the significance of RWC, MSI, chlorophyll content, and antioxidant enzymes in sustaining yield under drought stress. Broad-sense heritability estimates were high for key drought-related traits, particularly APX, SOD, and NGPS, indicating strong genetic potential for selection. These findings indicated the importance of integrating physiological and biochemical markers into breeding programs to develop high-yielding drought-tolerant wheat varieties, contributing to sustainable wheat production under water-limited conditions.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e19341"},"PeriodicalIF":2.3,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12087580/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144102397","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Emodin, a rising star in the treatment of glycolipid metabolism disorders: a preclinical systematic review and meta-analysis.","authors":"Yang Xiao, Zhixuan Zhao, Binqin Chen, Jian Sun, Li Wang, Yu Wang, Zheng Nan, Qi Zhang","doi":"10.7717/peerj.19221","DOIUrl":"10.7717/peerj.19221","url":null,"abstract":"<p><strong>Background: </strong>Rhubarb has a remarkable effect on lowering blood lipid and glucose levels, and its main component, emodin, is an anthraquinone derivative. To elucidate the role and mechanism of emodin in the treatment of type 2 diabetes mellitus (T2DM) and to provide robust evidence for its clinical application, we conducted a systematic review and meta-analysis to assess the influence of emodin on T2DM animal models and the overall therapeutic effect, and further to evaluate its benefits and risks in the management of T2DM.</p><p><strong>Methods: </strong>Eight databases were searched from inception to May 2023. Two reviewers extracted the data independently. SYRCLE's risk of bias tool for animal studies was used to assess the quality of articles. RevMan V.5.4 software and STATA 15.1 software were applied for data analyses. Body weight, serum insulin level (INS), fasting blood glucose (FBG), 2-hour postprandial blood glucose (2hPG, IPGTT/OGTT), insulin tolerance test (IPITT) indicators, total cholesterol (TC), triglycerides (TG), high-density lipoprotein (HDL-c), and low-density lipoprotein cholesterol (LDL-c) were used as outcome measures. Data for outcome messures presented in graphical form were extracted using GetData graphic digitizer software (version 2.26). For outcome indicators with a small number of included studies, we will conduct descriptive analyses.</p><p><strong>Results: </strong>Twelve existing studies were included in this meta-analysis, and all of the studies included in this review had a low to moderate risk of bias. The results showed that emodin significantly reduced the glucose and lipid metabolism indicators and effectively lowered body weight and serum insulin levels (FBG, 2hPG(IPGTT/OGTT), IPITT, TG, TC, LDL-c, HDL-c) (<i>P</i> < 0.05).</p><p><strong>Conclusion: </strong>Emodin demonstrates significant potential in treating T2DM by reducing FBG, 2hPG (IPGTT/OGTT), IPITT, TC, TG, INS, and body weight in animal models. The therapeutic mechanisms of emodin include enhancing glucose utilization in peripheral tissues, inhibiting glucosidase absorption, alleviating insulin resistance, and strengthening L-type calcium channels. Additionally, emodin shares characteristics with first-line antidiabetic drugs such as metformin, acarbose, and repaglinide, promoting insulin secretion and enhancing cellular sensitivity to insulin. Furthermore, emodin exhibits actions similar to glucagon-likepeptide-1(GLP-1) receptor agonists, suggesting its potential for protecting target organs. Therefore, emodin is a highly promising drug with substantial research and clinical value. However, caution should be exercised due to significant heterogeneity among the studies, and results may evolve with additional research.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e19221"},"PeriodicalIF":2.3,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12085882/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144094555","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"HD-6mAPred: a hybrid deep learning approach for accurate prediction of N6-methyladenine sites in plant species.","authors":"Huimin Li, Wei Gao, Yi Tang, Xiaotian Guo","doi":"10.7717/peerj.19463","DOIUrl":"10.7717/peerj.19463","url":null,"abstract":"<p><strong>Background: </strong>N6-methyladenine (6mA) is an important DNA methylation modification that serves a crucial function in various biological activities. Accurate prediction of 6mA sites is essential for elucidating its biological function and underlying mechanism. Although existing methods have achieved great success, there remains a pressing need for improved prediction accuracy and generalization cap ability across diverse species. This study aimed to develop a robust method to address these challenges.</p><p><strong>Methods: </strong>We proposed HD-6mAPred, a hybrid deep learning model that combines bidirectional gated recurrent unit (BiGRU), convolutional neural network (CNN) and attention mechanism, along with various DNA sequence coding schemes. Firstly, DNA sequences were encoded using four different ways: one-hot encoding, electron-ion interaction pseudo-potential (EIIP), enhanced nucleic acid composition (ENAC) and nucleotide chemical properties (NCP). Secondly, a hold-out search strategy was employed to identify the optimal features or feature combinations for both BiGRU and CNN. Finally, the attention mechanism was introduced to weigh the importance of features derived from the BiGRU and CNN.</p><p><strong>Results: </strong>A series of experiments on the <i>Rosaceae</i>, rice and <i>Arabidopsis</i> datasets were conducted to demonstrate the superiority of HD-6mAPred. In <i>Rosaceae</i>, the HD-6mAPred model achieved excellent performance: accuracy (ACC) of 0.996, Matthew correlation coefficient (MCC) of 0.993, sensitivity (SN) and specificity (SP) of 0.995 and 0.998, respectively. In rice, the evaluation metrics are 0.952 (ACC), 0.905 (MCC), 0.955 (SN), and 0.949 (SP). In <i>Arabidopsis</i>, the corresponding metrics are 0.937 (ACC), 0.875 (MCC), 0.927 (SN), and 0.948 (SP). Compared to existing methods, these results demonstrate that HD-6mAPred achieves state-of-the-art performance in predicting 6mA sites across three plant species. Furthermore, HD-6mAPred not only improves the accuracy of 6mA site prediction, but also shows excellent generalization capability across species. The source code utilized in this study is publicly accessible at https://doi.org/10.5281/zenodo.15355131.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e19463"},"PeriodicalIF":2.3,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12085883/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144094602","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Expected mortality risk for coho salmon landed in recreational troll fisheries using 1/0 and 6/0 hooks in the marine waters of Washington state.","authors":"Jonathan J Scordino, Ryan P Walsh, William Jasper, Deon J Roche, William Tyler","doi":"10.7717/peerj.19434","DOIUrl":"10.7717/peerj.19434","url":null,"abstract":"<p><p>Recreational salmon fisheries in the state of Washington are managed with size-selective and mark-selective rules to promote the release of wild and undersized salmon. In order for this management approach to be effective, the fishery must have low mortality of hooked and released salmon. In this study, we directly compared the fishing performance of small (1/0, 14.36 mm gap) and large (6/0, 17.20 mm gap) hooks in recreational salmon troll fisheries with the goal of evaluating differences in drop-off rates, size of salmon caught, and the probability a fish would be hooked in a region documented to have low, intermediary, or high risk of mortality. We found strong evidence that hook size affects the probability that an angler can land a fish with drop-off rates of 48.9% for fish hooked on small (1/0) hooks and 34.0% for fish hooked on large (6/0) hooks. There were no significant differences in the average length of pink, coho, or Chinook salmon caught on small (1/0) or large (6/0) hooks. Likewise, we found no significant differences in the proportion of coho and Chinook catch that were longer or shorter than their respective legal-size limits. Hook size did significantly affect the expected mortality risk of coho salmon with large (6/0) hooks being 1.82 times more likely to hook a salmon in body regions associated with high or intermediary risk of mortality than small (1/0) hooks. No significant differences were observed in the hooking rates of Chinook and pink salmon in body regions with high, intermediary, or low expected mortality risk, however our confidence in this finding is limited due to sample size. It is important to carefully assess whether these results support restrictions on hook sizes used in recreational coho salmon troll fisheries. The observation of reduced expected mortality risk of coho salmon landed using small (1/0) hooks as compared to when using large (6/0) hooks highlights the importance of evaluating the effect of hook size during recreational salmon troll fisheries on post-release survival and will hopefully stimulate more research on the effects of hook size and modeling on whether hook size regulations can improve salmon conservation.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e19434"},"PeriodicalIF":2.3,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12085881/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144094560","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Impact of forest fragmentation on river water quality: an example from a typical subtropical hilly basin.","authors":"Biao Li, Xiaolei Huang, Qiang Zhong, Xiuxiu Wu","doi":"10.7717/peerj.19435","DOIUrl":"10.7717/peerj.19435","url":null,"abstract":"<p><strong>Background: </strong>Forest fragmentation, driven by natural and human activities, is increasing. However, the impact of forest fragmentation on river water quality remains ambiguous.</p><p><strong>Methods: </strong>In this study, water quality data were collected from 15 monitoring sites in the upper Ganjiang River basin in winter and summer, and the forest landscape fragmentation metrics in the sub-basin was calculated to assess its seasonal impact on river water quality.</p><p><strong>Results: </strong>The results indicated that water quality in the area is generally satisfactory, with total nitrogen (TN) as the main pollutant. Redundancy analysis (RDA) showed that the explanation rate of the six forest landscape fragmentation metrics to the water quality change in summer was 41.21%, and in winter, their explanation rate of water quality change increased by 14.26%. Among them, the effective mesh size (MESH) was negatively correlated with most river water quality indicators, with a contribution rate of 20.9%. While the interspersion and juxtaposition index (IJI) was positively correlated with most water quality indicators in winter, with a contribution rate of 44.9%. It is worth noting that the thresholds for IJI and MESH of forest were the same in winter and summer, 28.1% and 7.89e+0.5ha, respectively, when the probability of an abrupt change in TN concentration reached 100%. This is implied that when the adjacency of forest patches is less than 28.1% and the connectivity of forest patches is more than 7.89e+0.5ha, it may contribute to the reduction of TN concentration in rivers. These findings provide valuable insights into how varying degrees of forest fragmentation can lead to deterioration in river water quality, and allow for further planning of forest structure based on forest fragmentation thresholds to improve regional water quality.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e19435"},"PeriodicalIF":2.3,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12085114/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144094611","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}